Just as the Omicron wave may have broken across the U.S. comes word of another version of the more transmissible variant, dubbed BA.2. It’s been nicknamed by some “stealth Omicron” because it seems to evade identification better than its predecessor.
While other new variants that seemed worrisome — like Mu or Lambda — have had little impact, and details remain sketchy, early indications are that BA.2 seems to be spreading even in countries where the original Omicron lineage, BA.1, is dominant.
In Denmark, a country whose Covid policies are often contrasted with the U.S., BA.2 now accounts for nearly half of the test samples sequenced. In the final week of December, according to data from Statens Serum Institut under the auspices of the Danish Ministry of Health, the subvariant accounted for 20% of all Covid cases in Denmark. By the second week of January, its share had risen to about 45% of the total.
“During the same period, the relative frequency of BA.1 has dropped,” according to a statement from the institute. “BA.1 and BA.2 have many differences in their mutations in the most important areas. In fact, the difference between BA.1 and BA.2 is greater than the difference between the original variant and the Alpha variant.”
An initial analysis instances of BA.2 in the country “shows no differences in hospitalisations,” according to SSI. It’s also unclear how effective the current vaccines are against the subvariant.
BA.2 “has been designated a variant under investigation” by the UK Health Security Agency. The new version of Omicron was first detected in the UK on December 6, 2021, per a HSA report. To date, there have been 426 confirmed cases, with the greatest concentration centered around London.
“Early analyses suggest an increased growth rate compared to BA.1, however, growth rates have a low level of certainty early in the emergence of a variant and further analysis is needed,” reads the report.
Those reports may also be inaccurate because UK officials suspect the offshoot may be harder to identify, since it does not display a telltale sign in PCR tests which has often indicated Omicron. While a PCR test would still come up with a general positive, such samples would need to be genomically sequenced, a much more costly and time-consuming process that is less common to ID the specific variant involved.
“Omicron BA.2 lacks the genetic deletion on the spike protein which produces S-gene target failure (SGTF) in some polymerase chain reaction (PCR) tests, which has been used as a proxy for Omicron cases previously,” reads the UK document.
The #OmicronVariant sub-lineage known as BA.2 has been designated as a variant under investigation. The number of BA.2 cases is currently low, with the original Omicron lineage, BA.1, still dominant in the UK and further analyses will now be undertaken. https://t.co/254m2rwJN5
— UK Health Security Agency (@UKHSA) January 21, 2022
“[I] think likely scenario is BA.2 just exacerbates what the national Omicron situation is,” said Tom Peacock, a virologist at Imperial College London.
BA.2 has protein differences from BA.1, potentially dozens, as estimated by Peacock. See the first and second lines of the accompanying chart from South African health officials for a general sense.
It has also been found in the U.S., according to Sinclair Broadcasting’s Seattle station, KOMO News, which reported the Washington State Health Department has confirmed two cases of BA.2 were “found earlier this month.”
“It’s too early to tell if we are going to see more cases of this variant,” WA health department spokesperson Shelby Anderson told the outlet. “So far, fewer than 100 confirmed BA.2 cases in the U.S. have been reported.”
At least three cases have been found at Houston’s Methodist Hospital, where genomic sequencing is more robust than elsewhere.
One anonymous Biden administration official, however, told the Washington Post on Monday that “there is concern about the omicron BA.2 variant.” Because of the increase in cases overseas, the person said the U.S. is gearing up and “paying close attention to the BA.2 variant.”